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genBaRcode

Analysis and Visualization Tools for Genetic Barcode Data

Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).

Functions (53)

BC_dat

Barcode distribution of an example experiment.

BC_dat_EC

Barcode distribution of an example experiment.

BCdat-class

BCdat class.

asBCdat

Data Type Conversion

com_pair

Compairing two BCdat Objects

createGDF

Creating a gdf File

dot-createPatternFile

Internal function

dot-generateColors

Color list generation

dot-getBarcodeFilter

Internal function

dot-getDiagonalIndex

Index Generation

dot-getMinDist

Distance calculation

dot-getWobblePos

getWobblePos

dot-hex2rgbColor

Converts hex colors into gephi usable rgb colors

dot-revComp

DNA string manipulation

dot-revComp_EqLength

DNA string manipulation for equal string sizes

dot-revComp_UneqLength

DNA string manipulation for unequal string sizes

dot-testDirIdentifier

Internal function

errorCorrection

Error Correction

error_correction_circlePlot

Circle Plot

error_correction_clustered_HDs

Clustered HD Plot

error_correction_treePlot

Tree Plot

extractBarcodes

Barcode extraction

genBaRcode_app

Shiny App

generateKirchenplot

Plotting a Kirchenplot

generateTimeSeriesData

Generating Time Series Data Object

getBackbone

Accessing the Barcode Backbone slot of a BCdat objects.

getBackboneSelection

Predefined Barcode Backbone Sequences

getLabel

Accessing the Label slot of a BCdat objects.

getReads

Accessing the Read-Count slot of a BCdat objects.

getResultsDir

Accessing the Results Directory slot of a BCdat objects.

ggplotDistanceGraph

Plotting a Distance Network

ggplotDistanceGraph_EC

Plotting a Distance Network (error correction)

hybridsIdentification

Identifies hybrid barcodes

plotClusterGgTree

Plotting a Cluster ggTree

plotClusterTree

Plotting a Cluster Tree

plotDistanceIgraph

Plotting a Distance Network

plotDistanceVisNetwork

Plotting a Distance Network

plotDistanceVisNetwork_EC

Plotting a Distance Network (error correction)

plotNucFrequency

Plotting Nucleotide Frequency

plotQualityScoreDis

Plotting Quality Score Distribution

plotQualityScorePerCycle

Plotting Quality Score per Cycle

plotReadFrequencies

Plotting a Barplot

plotSeqLogo

Plots a sequence logo

plotTimeSeries

Plotting Time Series Data

plotVennDiagram

Plotting a VennDiagram

prepareDatObject

Data Object Preparation

processingRawData

Data processing

qualityFiltering

Quality Filtering

readBCdat

Data Input

setBackbone

Replacing the Barcode Backbone slot of a BCdat objects.

setLabel

Replacing the Label slot of a BCdat objects.

setReads

Replacing the Read-Count slot of a BCdat objects.

setResultsDir

Replacing the Results Directory slot of a BCdat objects.

genBaRcode

Analysis and Visualization Tools for Genetic Barcode Data

v1.2.4
LGPL
Authors
Lars Thielecke <lars.thielecke@tu-dresden.de>
Initial release

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